Merge pull request #136 from bfrgoncalves/flowcraft_reports

Flowcraft reports

README.md

@@ -1,23 +1,39 @@
 # INNUENDO
+
 [![Documentation Status](https://readthedocs.org/projects/innuendo/badge/?version=latest)](https://innuendo.readthedocs.io/en/latest/?badge=latest)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/0fffb6e32a564841a1dfb9230616d5f6)](https://app.codacy.com/app/bfrgoncalves/INNUENDO_REST_API?utm_source=github.com&utm_medium=referral&utm_content=bfrgoncalves/INNUENDO_REST_API&utm_campaign=Badge_Grade_Dashboard)
 
 #### A novel cross-sectorial platform for the integration of genomics in surveillance of foodborne pathogens
 
-In this repository you will find all the necessary information regarding platform architecture, installation and source code.
+In this repository you will find all the necessary information regarding 
+platform architecture, installation and source code.
 
 > **Architecture**
 
-INNUENDO platform is divided into two distinct applications that comunicate between each other. The first one, the **INNUENDO frontend server**, comprises the user web interface and mechanisms to allow secure user authentication with LDAP and data storage into a dedicated database. It also comunicates with the **INNUENDO process controller**, which was developed with the aim of working as a bridge to allow running analytical procedures on a laptop or in a High Performance Computer (HPC), with the help of SLURM process manager.
+INNUENDO platform is divided into two distinct applications that communicate 
+between each other. The first one, the **INNUENDO frontend server**, comprises 
+the user web interface and mechanisms to allow secure user authentication 
+using LDAP (if required), and database communication. It also communicates 
+with the **INNUENDO process controller**, which was developed with the aim of working as 
+a bridge to allow running analytical procedures on a laptop or in a High 
+Performance Computer (HPC), with the help of SLURM process manager.
 
 In this repository you can find the source code regarding the **INNUENDO 
 frontend server** and its associated RESTful API.
 
 > **Installation**
 
-Information about the platform instalation can be found at the documentation.
+Information about the platform installation can be found at the documentation.
 
 > **Source code**
 
-* [**INNUENDO frontend server**](https://github.com/B-UMMI/INNUENDO_REST_API) 
-* [**INNUENDO process controller server**](https://github.com/B-UMMI/INNUENDO_PROCESS_CONTROLLER)
+* [**INNUENDO frontend server**](https://github.com/bfrgoncalves/INNUENDO_REST_API) 
+* [**INNUENDO process controller server**](https://github.com/bfrgoncalves/INNUENDO_PROCESS_CONTROLLER)
+
+> **Docker-Compose**
+
+A docker-compose version of the INNUENDO Platform is also available and can 
+be used for an easier deployment since it installs all the components 
+automatically.
+
+* [**Docker-Compose version**](https://github.com/bfrgoncalves/INNUENDO_docker)

app/__init__.py

@@ -29,7 +29,6 @@
         - app_configuration (before first request and override login post of the flask-login package to deal with ldap)
 '''
 
-
 # Setup app
 app = Flask(__name__)
 # Reads the config file located at ../
@@ -48,7 +47,6 @@ def simple(env, resp):
 # SET THE REDIS QUEUE
 q = Queue(connection=conn)
 
-
 from app.models.models import User, Role
 
 user_datastore = SQLAlchemyUserDatastore(db, User, Role)
@@ -60,7 +58,7 @@ def simple(env, resp):
 # setup agraph
 server = AllegroGraphServer(AG_HOST, AG_PORT, AG_USER, AG_PASSWORD)
 catalog = server.openCatalog()
-   
+
 myRepository = catalog.getRepository(AG_REPOSITORY, Repository.OPEN)
 myRepository.initialize()
 dbconAg = myRepository.getConnection()

app/api.py

@@ -39,7 +39,7 @@
     NGSOnto_ProcessListPipelineResource, NGSOnto_ProcessResource, \
     NGSOnto_ProcessJobID, NGSOnto_ProcessOutputResource
 from resources.jobs.jobs import Job_queue, Job_results, Job_Result_Download, \
-    Job_classify_chewbbaca, Job_Result_Download_click, Job_Reports, \
+    Job_Result_Download_click, Job_Reports, \
     NextflowLogs, Job_Report_Download_click, FlowcraftInspect
 from resources.phyloviz.phyloviz import PHYLOViZResource, TreeResource, \
     TreeUserResource, PHYLOViZJobResource, getProfilesResource, \
@@ -151,8 +151,6 @@
 api.add_resource(NextflowLogs, '/api/v1.0/jobs/logs/nextflow/')
 api.add_resource(FlowcraftInspect, '/api/v1.0/jobs/inspect/')
 
-api.add_resource(Job_classify_chewbbaca, '/api/v1.0/jobs/classify/')
-
 ################################# PHYLOVIZ REQUESTS ###########################
 
 api.add_resource(PHYLOViZResource, '/api/v1.0/phyloviz/')

app/app_configuration.py

@@ -10,16 +10,14 @@
 from flask import request, after_this_request, redirect, current_app
 from flask_security.utils import do_flash, get_message, get_url
 from flask_security.signals import password_changed
-from config import obo,localNSpace,dcterms, SFTP_HOST, LOGIN_METHOD, \
+from config import localNSpace,dcterms, SFTP_HOST, LOGIN_METHOD, \
     LOGIN_USERNAME, LOGIN_GID, LOGIN_HOMEDIR, LOGIN_PASSWORD, LOGIN_EMAIL, \
     ALL_SPECIES
 from franz.openrdf.vocabulary.rdf import RDF
 
-'''
-App configuration:
+'''App configuration:
     - Set of functions to be applied before the first app request and an 
-    handle  override for the flask-login post function
-'''
+    handle  override for the flask-login post function'''
 
 
 # Executes before the first request is processed.

app/models/models.py

@@ -3,13 +3,11 @@
 from app import db
 from flask_security import UserMixin, RoleMixin
 from sqlalchemy.dialects.postgresql import ARRAY, JSON
-from config import LDAP_PROVIDER_URL, baseDN, LDAP_ADMIN_NAME, LDAP_ADMIN_PASS
+from config import LDAP_PROVIDER_URL, baseDN, LDAP_ADMIN_PASS
 from passlib.hash import ldap_md5
 
-'''
-Models:
-    - Defines every model to be used on the postgres database
-'''
+'''Models:
+    - Defines every model to be used on the postgres database'''
 
 # Secondary role table
 roles_users = db.Table('roles_users',
@@ -129,14 +127,6 @@ def try_login(email, password):
         except Exception as e:
             return False
 
-        #conn.unbind()
-
-        '''try:
-            conn.simple_bind_s("cn=" + LDAP_ADMIN_NAME + "," + baseDN, LDAP_ADMIN_PASS)
-        except Exception as e:
-            print e
-            return False'''
-
         search_filter = "uid="+email
         entry = ""
         result = conn.search_s(baseDN, ldap.SCOPE_SUBTREE, search_filter)

app/resources/file_resources/file_resources.py

@@ -1,13 +1,11 @@
-from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
-from flask import jsonify, send_file
+from flask_restful import Resource, reqparse
+from flask import send_file
 
-from flask_security import current_user, login_required, roles_required, auth_token_required
+from flask_security import login_required
 import os
 
-'''
-File resources:
-    - Get template for strain batch submission
-'''
+'''File resources:
+    - Get template for strain batch submission'''
 
 
 class TemplateResource(Resource):

app/resources/jobs/checks.py

@@ -1,5 +1,5 @@
 from app import db
-from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
+from flask_restful import Api, Resource, reqparse, abort, marshal_with
 from config import JOBS_ROOT, LDAP_PROVIDER_URL, phyloviz_root
 import ldap
 from app.models.models import Ecoli, Project, Platform
@@ -8,7 +8,7 @@
 from flask_security import current_user
 
 # Imports for allegrograph check
-from config import AG_HOST, AG_PORT, AG_REPOSITORY, AG_USER, AG_PASSWORD
+from config import AG_HOST, AG_PORT, AG_USER, AG_PASSWORD
 from franz.openrdf.sail.allegrographserver import AllegroGraphServer
 
 
@@ -31,8 +31,9 @@ def get(self):
 
         try:
             project = db.session.query(Project).first()
-
+            print project
         except Exception as e:
+            print e
             return False
 
         return True
@@ -44,8 +45,9 @@ def get(self):
 
         try:
             project = db.session.query(Ecoli).first()
-
+            print project
         except Exception as e:
+            print e
             return False
 
         return True

app/resources/jobs/jobs.py

@@ -5,7 +5,7 @@
 from flask_security import current_user, login_required, roles_required, auth_token_required
 import datetime
 from config import CURRENT_ROOT, JOBS_ROOT, OUTPUT_URL, USER_STORAGES
-from config import obo,localNSpace,protocolsTypes,processTypes,processMessages
+from config import obo,localNSpace
 from franz.openrdf.query.query import QueryLanguage
 from app.models.models import Protocol
 from app.models.models import Strain
@@ -611,29 +611,6 @@ def get(self):
         return report.report_data
 
 
-# Load job results and classify it
-class Job_classify_chewbbaca(Resource):
-    """
-    Class to classify chewbbaca
-    """
-
-    def get(self):
-        """Classify profile
-
-        Classify a profile by giving its job_id
-
-        (DEPRECATED)
-
-        Returns
-        -------
-
-        """
-
-        args = job_classify_chewbbaca_post_parser.parse_args()
-        database_processor.classify_profile(args.job_id,
-                                            args.database_to_include)
-
-
 # Load job results to display on graphical interface
 class Job_Result_Download(Resource):
 

app/resources/ngs_onto/ngs_onto_pipelines.py

@@ -1,6 +1,6 @@
 from app import dbconAg
 from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
-from flask_security import current_user, login_required
+from flask_security import login_required
 from app.utils.queryParse2Json import parseAgraphStatementsRes
 
 from config import obo,localNSpace,protocolsTypes,processTypes,processMessages

app/resources/ngs_onto/ngs_onto_processes.py

@@ -299,11 +299,6 @@ def post(self, id, id2):
             pprocid = args.parent_process_id
             rpipid = args.real_pipeline_id
 
-            parentProcessURI = dbconAg.createURI(
-                namespace=localNSpace+"projects/",
-                localname=str(ppropid)+"/pipelines/" +
-                          str(ppipid)+"/processes/"+str(pprocid))
-
         if ppipid == rpipid:
             for proc_json in procJsonResult:
                 if int(proc_json["StrIndex"].replace('"', '')) > int(pprocid):

app/resources/ngs_onto/ngs_onto_projects.py

@@ -2,7 +2,7 @@
 from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
 from app.utils.queryParse2Json import parseAgraphStatementsRes
 from flask_security import current_user, login_required, roles_required
-from config import obo,localNSpace,protocolsTypes,processTypes,processMessages
+from config import obo,localNSpace, processTypes,processMessages
 from franz.openrdf.vocabulary.rdf import RDF
 
 

app/resources/ngs_onto/ngs_onto_protocols.py

@@ -1,5 +1,5 @@
 from app import dbconAg
-from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
+from flask_restful import Resource, reqparse, abort, fields
 from flask_security import current_user, login_required
 from app.utils.queryParse2Json import parseAgraphQueryRes
 from config import obo,localNSpace,protocolsTypes,processTypes,processMessages

app/resources/ngs_onto/ngs_onto_strains.py

@@ -1,7 +1,7 @@
 from app import dbconAg
 from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
 from app.utils.queryParse2Json import parseAgraphStatementsRes
-from flask_security import current_user, login_required, roles_required
+from flask_security import login_required, roles_required
 from config import obo,localNSpace,protocolsTypes,processTypes,processMessages
 from franz.openrdf.vocabulary.rdf import RDF
 

app/resources/ngs_onto/ngs_onto_users.py

@@ -1,7 +1,7 @@
 from app import dbconAg,dedicateddbconAg
 from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
-from flask_security import current_user, login_required
-from config import obo,localNSpace,dcterms
+from flask_security import login_required
+from config import localNSpace,dcterms
 from franz.openrdf.vocabulary.rdf import RDF
 from app.utils.queryParse2Json import parseAgraphStatementsRes
 

app/resources/ngs_onto/ngs_onto_workflows.py

@@ -1,5 +1,5 @@
 from app import dbconAg
-from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
+from flask_restful import Resource, reqparse, fields
 from app.utils.queryParse2Json import parseAgraphStatementsRes,parseAgraphQueryRes
 from config import obo,localNSpace,protocolsTypes,processTypes,processMessages
 from franz.openrdf.vocabulary.rdf import RDF

app/resources/phyloviz/phyloviz.py

@@ -2,7 +2,7 @@
 from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
 from flask_security import current_user, login_required, roles_required, \
     auth_token_required
-from config import CURRENT_ROOT, JOBS_ROOT, phyloviz_root
+from config import JOBS_ROOT, phyloviz_root
 from app.models.models import Tree
 import requests
 import os

app/resources/postgres/messages.py

@@ -1,7 +1,7 @@
 from app import db, mail
 from app.models.models import Message, User
 from flask_restful import Api, Resource, reqparse, abort, fields, marshal_with
-from flask_security import current_user, login_required, roles_required
+from flask_security import current_user, login_required
 from sqlalchemy import desc
 import datetime
 
@@ -245,6 +245,7 @@ def post(self):
             mail.send(msg)
 
         except Exception as e:
+            print e
             return False
 
         return True

app/resources/postgres/processes.py

@@ -6,12 +6,9 @@
 
 ############################################ NOT BEING USED ####################
 
-"""
-Processes are being defined in the ngsonto resources
+"""Processes are being defined in the ngsonto resources
 
-DEPRECATED
-
-"""
+DEPRECATED"""
 
 # Defining post arguments parser
 process_post_parser = reqparse.RequestParser()

app/resources/postgres/projects.py

@@ -1,10 +1,10 @@
 from app import db
-from flask_restful import Api, Resource, reqparse, abort, fields, \
-    marshal_with #filters data according to some fields
+# filters data according to some fields
+from flask_restful import Resource, reqparse, abort, fields, \
+    marshal_with
 
 from app.models.models import Project, User
-from flask_security import current_user, login_required, roles_required, \
-    auth_token_required
+from flask_security import current_user, login_required, roles_required
 import datetime
 import random
 import string
@@ -249,13 +249,13 @@ def post(self):
                           name=args.name,
                           timestamp=datetime.datetime.utcnow())
         if not project:
-            abort(404, message="An error as occurried when uploading the data"
-                  .format(id))
+            abort(404, message="An error as occurried when uploading the data")
 
         try:
             db.session.add(project)
             db.session.commit()
         except Exception as e:
+            print e
             abort(409, message="Project name already exists.")
         return project, 201
 

app/resources/postgres/protocols.py

@@ -1,5 +1,5 @@
 from app import db
-from flask_restful import Api, Resource, reqparse, abort, fields, \
+from flask_restful import Resource, reqparse, abort, fields, \
     marshal_with  # filters data according to some fields
 
 import json
@@ -19,9 +19,7 @@
 protocol_post_parser.add_argument('version', dest='version', type=str,
                                   required=True, help="Protocol version")
 
-"""
-STEPS -> Parameters which define the protocol
-"""
+"""STEPS -> Parameters which define the protocol"""
 
 # Defining get arguments parser
 protocol_get_parser = reqparse.RequestParser()